Magnesium in PDB 6lyf: Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met)

The structure of Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met), PDB code: 6lyf was solved by K.H.Park, E.J.Woo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.200, 81.880, 88.657, 90.00, 97.59, 90.00
R / Rfree (%)	19.9 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met) (pdb code 6lyf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met), PDB code: 6lyf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:69.0 occ:1.00 O A:HOH406 2.2 76.0 1.0 O A:HOH422 2.3 37.2 1.0 OD1 A:ASN169 2.3 32.5 1.0 O A:HOH410 2.3 48.7 1.0 O A:HOH417 2.5 19.1 1.0 O A:HOH436 3.4 44.3 1.0 CG A:ASN169 3.5 29.7 1.0 N A:ALA138 3.9 34.1 1.0 O A:ALA138 4.0 30.6 1.0 OE1 A:GLN164 4.0 43.6 1.0 O A:ASN169 4.1 49.2 1.0 OE1 A:GLU177 4.1 66.5 1.0 ND2 A:ASN169 4.2 31.6 1.0 CA A:GLY137 4.2 26.6 1.0 OE2 A:GLU177 4.2 61.2 1.0 C A:GLY137 4.4 31.2 1.0 CD1 A:TRP173 4.5 33.6 1.0 CD A:GLU177 4.6 58.9 1.0 CB A:ASN169 4.6 30.2 1.0 CA A:ALA138 4.7 32.9 1.0 C A:ALA138 4.8 31.3 1.0 CA A:ASN169 4.8 33.1 1.0 C A:ASN169 4.8 46.1 1.0 CB A:ALA138 4.9 19.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:74.0 occ:1.00 ND2 B:ASN169 2.1 59.5 1.0 O B:HOH426 2.7 51.7 1.0 CG B:ASN169 3.0 57.0 1.0 OD1 B:ASN169 3.2 60.9 1.0 O B:HOH415 3.2 41.2 1.0 N B:ALA138 3.9 46.1 1.0 CA B:GLY137 4.1 36.0 1.0 O B:HOH427 4.4 50.0 1.0 CB B:ASN169 4.4 56.4 1.0 O B:ARG136 4.5 46.9 1.0 C B:GLY137 4.5 45.7 1.0 O B:ASN169 4.5 60.7 1.0 OE1 B:GLN164 4.7 55.4 1.0 O B:ALA138 4.7 45.6 1.0 OE2 B:GLU177 4.9 72.8 1.0 CA B:ALA138 4.9 45.7 1.0 CB B:ALA138 4.9 43.7 1.0 OE1 B:GLU177 4.9 75.8 1.0 CA B:ASN169 5.0 57.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:58.6 occ:1.00 ND2 C:ASN169 2.2 45.3 1.0 O C:HOH426 2.3 27.9 1.0 O C:HOH417 2.4 28.8 1.0 O C:HOH419 2.5 64.7 1.0 O C:HOH429 2.7 37.8 1.0 CG C:ASN169 3.3 33.4 1.0 OD1 C:ASN169 3.7 30.8 1.0 N C:ALA138 4.0 29.4 1.0 O C:ASN169 4.2 31.0 1.0 CA C:GLY137 4.2 21.5 1.0 OE1 C:GLU177 4.2 29.8 1.0 OE1 C:GLN164 4.2 41.2 1.0 OE2 C:GLU177 4.2 29.9 1.0 O C:ALA138 4.3 39.4 1.0 O C:HOH411 4.4 25.8 1.0 O C:HOH459 4.4 18.1 1.0 C C:GLY137 4.5 24.0 1.0 CD C:GLU177 4.6 26.7 1.0 CB C:ASN169 4.6 31.0 1.0 CA C:ASN169 4.9 30.5 1.0 C C:ASN169 4.9 29.3 1.0 CA C:ALA138 5.0 29.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Mouse Endonuclease Endog(H138A/Se-Met) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:56.3 occ:1.00 OD1 D:ASN169 2.5 37.1 1.0 O D:HOH416 2.6 37.6 1.0 OE1 D:GLN164 3.0 37.7 1.0 O D:ALA138 3.3 24.6 1.0 O D:HOH437 3.5 24.1 1.0 N D:ALA138 3.5 23.9 1.0 CG D:ASN169 3.6 27.2 1.0 CA D:GLY137 3.7 20.3 1.0 CD1 D:TRP173 3.7 33.4 1.0 OE2 D:GLU177 3.8 46.0 1.0 C D:GLY137 3.8 26.5 1.0 CD D:GLN164 4.0 33.6 1.0 NE1 D:TRP173 4.1 33.8 1.0 C D:ALA138 4.1 24.2 1.0 NE2 D:GLN164 4.4 30.4 1.0 CA D:ALA138 4.4 21.2 1.0 CB D:ASN169 4.5 23.9 1.0 O D:ASN169 4.5 37.2 1.0 ND2 D:ASN169 4.5 28.2 1.0 CD D:GLU177 4.6 39.1 1.0 CA D:ASN169 4.6 27.2 1.0 O D:GLY137 4.7 27.7 1.0 CG D:TRP173 4.7 32.9 1.0 OE1 D:GLU177 4.8 46.3 1.0 CB D:ALA138 5.0 17.4 1.0

K.H.Park, S.M.Yoon, H.N.Song, J.H.Yang, S.E.Ryu, E.J.Woo. Crystal Structure of the Mouse Endonuclease G. Biochem.Biophys.Res.Commun. V. 526 35 2020.
ISSN: ESSN 1090-2104
PubMed: 32192768
DOI: 10.1016/J.BBRC.2020.03.060